Summary of Study ST003492
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002141. The data can be accessed directly via it's Project DOI: 10.21228/M8VZ4T This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003492 |
| Study Title | Metabolomic profiling of the secretome in normal primary human pulmonary artery smooth muscle cells |
| Study Summary | Growth medium of human pulmonary artery smooth muscle cells (PASMCs) was conditioned for 24 hours and analyzed by LC-MS, termed conditioned medium (CM). Comparing to fresh complete vascular smooth muscle cell growth medium (GM), LC-MS profiling screened 138 metabolites and identified that three branched chain alpha-ketoacids, namely KIC, KIV, and KMV are the most abundant metabolites in CM of human PASMCs. |
| Institute | Peking University |
| Department | Department of Toxicology |
| Last Name | Xiao |
| First Name | Wusheng |
| Address | 38 Xueyuan Rd, Haidian District, Beijing, Beijing, 100191, China |
| wxiao@bjmu.edu.cn | |
| Phone | +1-010-82801628 |
| Submit Date | 2023-08-07 |
| Analysis Type Detail | MALDI |
| Release Date | 2024-10-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002141 |
| Project DOI: | doi: 10.21228/M8VZ4T |
| Project Title: | Secretome of normal primary human pulmonary artery smooth muscle cells |
| Project Summary: | This project aims to delineate the possible mediators of aerobic activation of HIF1alpha in normal primary cells and its biological consequences related to pulmonary vascular pathobiology. |
| Institute: | Peking University |
| Department: | Department of Toxicology |
| Laboratory: | WXIAO |
| Last Name: | Xiao |
| First Name: | Wusheng |
| Address: | 38 Xueyuan Rd, Haidian District, Beijing, Beijing, 100191, China |
| Email: | wxiao@bjmu.edu.cn |
| Phone: | +1-010-82801628 |
Subject:
| Subject ID: | SU003620 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Sample source |
|---|---|---|---|
| SA384072 | CMfromSMC 04 | CM | Vascular smooth muscle cells |
| SA384073 | CMfromSMC 05 | CM | Vascular smooth muscle cells |
| SA384074 | CMfromSMC 06 | CM | Vascular smooth muscle cells |
| SA384075 | SmGM 01 | GM | Vascular smooth muscle cells |
| SA384076 | SmGM 02 | GM | Vascular smooth muscle cells |
| SA384077 | SmGM 03 | GM | Vascular smooth muscle cells |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO003613 |
| Collection Summary: | Human primary pulmonary artery smooth muscle cells were cultured in complete vascular smooth muscle cell growth medium in a T75 flask. When cells reach to roungly 80% confluence, growth medium were refreshed with 10 mL and cultured for 24 hours. Medium samples were then collected and used for LC-MS analysis after centrifugation and removal of cell debris. |
| Sample Type: | Vascular smooth muscle cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003629 |
| Treatment Summary: | Human primary pulmonary artery smooth muscle cells were cultured in complete vascular smooth muscle cell growth medium in a T75 flask. When cells reach to roungly 80% confluence, growth medium were refreshed with 10 mL and cultured for 24 hours. Medium samples were then collected (termed conditioned medium, CM) and used for LC-MS analysis after centrifugation and removal of cell debris. Regular complete growth medium (GM) of vascular smooth muscle cells was included for comparison. |
| Treatment: | Conditioned medium (CM) vs regular growth medium (GM) |
| Treatment Compound: | N/A |
| Treatment Route: | N/A |
| Treatment Dose: | N/A |
| Treatment Dosevolume: | N/A |
| Treatment Doseduration: | 24 hours |
| Treatment Vehicle: | N/A |
| Cell Growth Container: | 75 cm flasks |
| Cell Growth Config: | 1200 rpm |
| Cell Growth Rate: | 30-40 hours |
| Cell Media: | Complete vascular smooth muscle cell growth medium supplemented with growth factors and 5% FBS |
| Cell Envir Cond: | 37 C and 5% CO2 |
| Cell Pct Confluence: | 70-80% |
| Cell Media Lastchanged: | Every 48 hours |
Sample Preparation:
| Sampleprep ID: | SP003627 |
| Sampleprep Summary: | Metabolites in equal volume of GM and CM were extracted using 100% -80 degree prechilled LC-MS grade methanol. The final concentration of methanol was 80%. Proteins were removed by centrifugation and supernatants were collected and evaporate on an Integrated SpeedVac System to the starting volume (~200 uL). Twenty microliters of the resulting medium samples were loaded into a LC-MS sampling tube for analysis. |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | Described in summary |
Combined analysis:
| Analysis ID | AN005732 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Merck ZIC-pHILIC(150 mm × 2.1 mm,3.5um) |
| MS Type | MALDI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Thermo Q Exactive Focus |
| Ion Mode | UNSPECIFIED |
| Units | ion intensity |
Chromatography:
| Chromatography ID: | CH004351 |
| Chromatography Summary: | Vanquish ultra-high performance liquid chromatography system coupled to a Q Exactive mass spectrometer |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Merck ZIC-pHILIC(150 mm × 2.1 mm,3.5um) |
| Column Temperature: | 4 |
| Flow Gradient: | gradient (%B) was 0 min, 80%; 20 min, 20%; 20.5 min, 80%; 28 min, 80%; and 42 min |
| Flow Rate: | 100 |
| Solvent A: | 100% water; 20 mM ammonium carbonate; 0.1% ammonium hydroxide |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005455 |
| Analysis ID: | AN005732 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Triple quadrupole |
| MS Type: | MALDI |
| MS Comments: | The mass spectrometer was operated in polarity-switching full scan mode from 70-1000 m/z. Resolution was set to 70,000, and the AGC target was 1×106 ions. Data were acquired and analyzed using TraceFinder 4.1 (Thermo) with peak identifications based on an in-house library of authentic metabolite standards previously analyzed utilizing this method. Missing values were imputed using random forest. Sample peak areas were normalized using probabilistic quotient normalization |
| Ion Mode: | UNSPECIFIED |
